Transcriptome

Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

X. F. Zheng, You, Y. N., Diao, Y., Zheng, X. W., Xie, K. Q., Zhou, M. Q., Hu, Z. L., and Wang, Y. W., “Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq”, vol. 14, pp. 11171-11184, 2015.

Nelumbo nucifera is an important economic vegetable and traditional medicine, but available genetic resources remain limited. Next generation sequencing has proven to be a rapid and effective means of identifying genic simple sequence repeat (genic-SSR) markers. This study developed genic-SSRs for N. nucifera using Illumina sequencing technology to assess diversity across cultivated and wild lotus. A total of 105,834 uni-contigs were produced with an average read length of 722 bp. Exactly 11,178 genic-SSR loci were identified in 9523 uni-contigs.

First transcriptional survey of the Malpighian tubules of giant mealworm, Zophobas morio (Coleoptera: Tenebrionidae)

J. R. Silva, Prado, R. A., Amaral, D. T., and Viviani, V. R., “First transcriptional survey of the Malpighian tubules of giant mealworm, Zophobas morio (Coleoptera: Tenebrionidae)”, vol. 14, pp. 464-473, 2015.

The Malpighian tubules play a key role in insect osmoregulation. Although a transcriptional analysis has been done for the Malpighian tubules in Drosophila melanogaster (Diptera), no functional genomics analysis has yet been carried out for any Coleoptera species. Recently, we constructed a cDNA library from Malpighian tubules of larval Zophobas morio, a close relative of Tribolium castaneum, and cloned the cDNA for an AMP/CoA-ligase with luciferase-like enzyme properties. Using this cDNA library, we randomly isolated, partially sequenced and analyzed ca.

Transcriptome analysis of skeletal muscle at prenatal stages in Polled Dorset versus Small-tailed Han sheep

N. Liu, He, J. N., Yu, W. M., Liu, K. D., Cheng, M., Liu, J. F., He, Y. H., Zhao, J. S., and Qu, X. X., “Transcriptome analysis of skeletal muscle at prenatal stages in Polled Dorset versus Small-tailed Han sheep”, vol. 14, pp. 1085-1095, 2015.

The objectives of the present study were to identify additional genes that may play important roles in the regulation of skeletal muscle growth and development, and to provide fundamental information for understanding the underlying molecular mechanisms. Eighteen cDNA libraries were constructed from the longissimus muscle of Polled Dorset (PD) and Small-tailed Han (SH) fetuses. To reveal the differences between the two species, we analyzed the differences in gene expression in 60-, 90- and 120-day fetal skeletal muscle by applying Agilent ovine genome-wide microarray.

Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica

S. T. Ivamoto, Domingues, D. S., Vieira, L. G. E., and Pereira, L. F. P., “Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica”, vol. 14, pp. 2399-2412, 2015.

Cytochrome P450s (P450s) comprise a gene superfamily encoding enzymes that are involved in diverse plant metabolic pathways that produce primary and secondary metabolites such as phenylpropanoids, terpenoids, nitrogen-containing compounds, and plant hormones. They comprise one of the most diverse gene families in plant evolution.

Transcriptome analysis of Arabidopsis seedlings responses to high concentrations of glucose

L. Han, Li, J. L., Jin, M., and Su, Y. H., “Transcriptome analysis of Arabidopsis seedlings responses to high concentrations of glucose”, vol. 14, pp. 4784-4801, 2015.

Sugars acting as fuel energy or as signaling molecules play important roles in plant growth and development. Although sugars associated with early seedling development have been analyzed in detail, few studies have examined the effect of sugar on genome-wide gene transcription. To analyze the role of glucose on the genomic level, we examined the response of seedlings to 5% glucose using RNA-seq technology. High concentrations of glucose significately altered the expression of 863 genes, with 558 upregulated and 305 downregulated genes by more than 2-fold.

Differential gene expression in pre-laying and laying period ovaries of Sichuan White geese (Anser cygnoides)

N. Ding, Han, Q., Zhao, X. Z., Li, Q., Li, J., Zhang, H. F., Gao, G. L., Luo, Y., Xie, Y. H., Su, J., and Wang, Q. G., “Differential gene expression in pre-laying and laying period ovaries of Sichuan White geese (Anser cygnoides)”, vol. 14, pp. 6773-6785, 2015.

Geese are an economically important poultry species worldwide. Their superior meat production performance and meat qual­ity make them a popular food. However, they are not bred worldwide because their poor laying capacity increases farming costs. To gain a global view of the genes that are differentially expressed between pre-laying (P) and laying (L) periods and to develop a database for further studies, we performed large-scale transcriptome sequencing of ovarian tissue collected from Anser cygnoides.

Gene expression characteristics of growth-inhibited rice seedlings induced by low-energy N+-beam implantation

H. Ya, Chen, Q., Wang, W., and Cheng, Y., “Gene expression characteristics of growth-inhibited rice seedlings induced by low-energy N+-beam implantation”, vol. 13, pp. 6259-6271, 2014.

Using the RNA sequencing, transcriptomes of growth-inhibited rice seedlings induced by low-energy N+-beam implantation were analyzed. The results showed that rice genes related to binding, electron carrier activity, transcription factor, auxin signal transduction, photosynthesis, and oxidoreductase activity were involved in the response to ion-beam implantation. Moreover, low-energy N+-beam implantation can induce the reactivation of the repressed rice transposable elements. These data are a useful resource for plant ion-beam implantation research.

RNA-seq reveals the downregulated proteins related to photosynthesis in growth-inhibited rice seedlings induced by low-energy N+ beam implantation

Q. F. Chen, Ya, H. Y., Wang, W. D., and Jiao, Z., “RNA-seq reveals the downregulated proteins related to photosynthesis in growth-inhibited rice seedlings induced by low-energy N+ beam implantation”, vol. 13, pp. 7029-7036, 2014.

Transcriptomic research based on RNA sequencing (RNA-seq) technology is innovative and will provide new opportunities and biological perspectives for the use of ion-beam implantation in plants. Using RNA-seq, transcriptomes of whole rice seedlings generated from seeds implanted with a low-energy N+ beam were analyzed 96 h after planting. We identified 544 transcripts that were differentially expressed genes (DEGs) in the non-growth-inhibited sample implanted by an N+ beam, including 262 upregulated transcripts and 282 downregulated transcripts.

Development and characterization of novel SSR markers in Siniperca kneri Garman

M. Yang, Zheng, H. Z., Liang, X. - F., Tian, C. X., Dou, Y. Q., Zhu, K. C., and Yuan, Y. C., “Development and characterization of novel SSR markers in Siniperca kneri Garman”, vol. 13, pp. 7593-7606, 2014.

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. The average allele number per locus was 5.1 (range: 2-8) for transcriptome-derived SSRs and 3.8 (range: 2-5) for genomic SSRs. The average observed and expected heterozygosities were 0.666 (range: 0.000-1.000) and 0.692 (range: 0.230-0.857) for transcriptome-derived SSRs, respectively. These values were 0.380 (range: 0.000-1.000) and 0.527 (range: 0.201-0.799) for genomic SSRs, respectively.

High-throughput sequencing identification of genes involved with Varroa destructor resistance in the eastern honeybee, Apis cerana

T. Ji, Yin, L., Liu, Z., Shen, F., and Shen, J., “High-throughput sequencing identification of genes involved with Varroa destructor resistance in the eastern honeybee, Apis cerana”, vol. 13, pp. 9086-9096, 2014.

Varroa destructor is the greatest threat to the honeybee Apis mellifera worldwide, while it rarely causes serious harm to its native host, the Eastern honeybee Apis cerana. The genetic mechanisms underlying the resistance of A. cerana to Varroa remain unclear. Thus, understanding the molecular mechanism of resistance to Varroa may provide useful insights for reducing this disease in other organisms. In this study, the transcriptomes of two A. cerana colonies were sequenced using the Illumina Solexa sequencing method.

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